Sweep: Refactor generally to improve quality the file individual.php and maintainbility plus readable by following psr standards about php-dna

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php-dna/src/Individual.php

Lines 1 to 84 in 3d5b908

	<?php
	require_once 'snps.php';
	require_once 'snps/utils.php';
	class Individual extends SNPs
	{
	/**
	* Object used to represent and interact with an individual.
	*
	* The ``Individual`` object maintains information about an individual. The object provides
	* methods for loading an individual's genetic data (SNPs) and normalizing it for use with the
	* `lineage` framework.
	*
	* ``Individual`` inherits from ``snps.SNPs``.
	*/
	private string $_name;
	public function __construct(string $name, mixed $raw_data = [], array $kwargs = [])
	{
	/**
	* Initialize an ``Individual`` object.
	*
	* Parameters
	* ----------
	* name : str
	* name of the individual
	* raw_data : str, bytes, ``SNPs`` (or list or tuple thereof)
	* path(s) to file(s), bytes, or ``SNPs`` object(s) with raw genotype data
	* kwargs : array
	* parameters to ``snps.SNPs`` and/or ``snps.SNPs.merge``
	*/
	$this->_name = $name;
	$init_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs);
	$merge_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, ''), $kwargs);
	parent::__construct(...array_values($init_args));
	if (!is_array($raw_data)) {
	$raw_data = [$raw_data];
	}
	foreach ($raw_data as $file) {
	$s = $file instanceof SNPs ? $file : new SNPs($file, ...array_values($init_args));
	$this->merge([$s], ...array_values($merge_args));
	}
	}
	private function _get_defined_kwargs(ReflectionMethod $callable, array $kwargs): array
	{
	$parameters = $callable->getParameters();
	$defined_kwargs = [];
	foreach ($parameters as $parameter) {
	$name = $parameter->getName();
	if (array_key_exists($name, $kwargs)) {
	$defined_kwargs[$name] = $kwargs[$name];
	}
	}
	return $defined_kwargs;
	}
	public function __toString(): string
	{
	return sprintf("Individual('%s')", $this->_name);
	}
	public function getName(): string
	{
	/**
	* Get this ``Individual``'s name.
	*
	* Returns
	* -------
	* str
	*/
	return $this->_name;
	}
	public function getVarName(): string
	{
	return clean_str($this->_name);

php-dna/src/Snps/Utils.php

Lines 1 to 196 in 3d5b908

	<?php
	/**
	* php-dna.
	*
	* Utility functions.
	*
	* @author Devmanateam <[email protected]>
	* @copyright Copyright (c) 2020-2023, Devmanateam
	* @license MIT
	*
	* @link http://github.com/familytree365/php-dna
	*/
	namespace Dna\Snps;
	use Exception;
	use ZipArchive;
	use Dna\Snps\Utils;
	/**
	* The Singleton class defines the `GetInstance` method that serves as an
	* alternative to constructor and lets clients access the same instance of this
	* class over and over.
	*/
	// from multiprocessing import Pool; // You can use parallel or pthreads for multi-processing in PHP
	// import os; // PHP has built-in OS functions
	// import re; // PHP has built-in RegExp functions
	// import shutil; // PHP has built-in filesystem functions
	// import tempfile; // PHP has built-in temporary file functions
	// import zipfile; // PHP has built-in ZipArchive class available
	// from atomicwrites import atomic_write; // You can use a library or implement atomic writes in PHP
	// import pandas as pd; // There is no direct PHP alternative to pandas; consider using array functions or a data manipulation library
	class Parallelizer
	{
	private bool $_parallelize;
	private ?int $_processes;
	public function __construct(bool $parallelize = false, ?int $processes = null): void
	{
	$this->_parallelize = $parallelize;
	/**
	* Utils class provides utility functions for file manipulation, parallel processing,
	* and other common tasks. It includes methods for gzipping files, creating directories,
	* fetching current UTC time, saving data as CSV, cleaning strings, and zipping files.
	*/
	$this->_processes = $processes ?? os_cpu_count();
	}
	public function __invoke(callable $f, array $tasks): array
	{
	if ($this->_parallelize) {
	// PHP does not have built-in support for parallel processing similar to Python's multiprocessing.
	// Consider using alternative approaches or libraries for parallel processing in PHP.
	// This example code is commented out as it requires the "parallel" PECL extension.
	// $runtime = new \parallel\Runtime();
	// $futures = [];
	// foreach ($tasks as $task) {
	// $futures[] = $runtime->run($f, [$task]);
	// }
	// return array_map(fn($future) => $future->value, $futures);
	return array_map($f, $tasks); // Fallback to sequential processing
	} else {
	return array_map($f, $tasks);
	}
	}
	function os_cpu_count(): int
	{
	// Use this function if you need to get the number of CPU cores in PHP
	// You might need to adjust this code based on your environment
	if (substr(php_uname('s'), 0, 7) == 'Windows') {
	return (int) shell_exec('echo %NUMBER_OF_PROCESSORS%');
	} else {
	return (int) shell_exec('nproc');
	}
	}
	}
	class Utils
	{
	public static function gzip_file(string $src, string $dest): string
	{
	/**
	* Gzip a file.
	*
	* @param string $src Path to file to gzip
	* @param string $dest Path to output gzip file
	*
	* @return string Path to gzipped file
	*/
	$bufferSize = 4096;
	$srcFile = fopen($src, "rb");
	if ($srcFile === false) {
	throw new Exception("Cannot open source file");
	}
	try {
	$destFile = fopen($dest, "wb");
	if ($destFile === false) {
	throw new Exception("Cannot create destination file");
	}
	try {
	$gzFile = gzopen($dest, "wb");
	if ($gzFile === false) {
	throw new Exception("Cannot create gzipped file");
	}
	try {
	while (!feof($srcFile)) {
	$buffer = fread($srcFile, $bufferSize);
	gzwrite($gzFile, $buffer);
	}
	} finally {
	gzclose($gzFile);
	}
	} finally {
	fclose($destFile);
	}
	} finally {
	fclose($srcFile);
	}
	return $dest;
	}
	}
	/**
	* Creates a directory if it doesn't exist.
	*
	* @param string $path Path to the directory to create.
	* @return void
	*/
	public static function create_dir(string $path): void
	{
	if (!file_exists($path)) {
	mkdir($path, 0777, true);
	}
	}
	/**
	* Gets the current UTC time.
	*
	* @return string Current UTC time in 'Y-m-d H:i:s' format.
	*/
	public static function get_utc_now(): string
	{
	return gmdate('Y-m-d H:i:s');
	}
	/**
	* Saves data as a CSV file.
	*
	* @param array $data Data to save.
	* @param string $filename Path to the CSV file.
	* @return void
	*/
	public static function save_df_as_csv(array $data, string $filename): void
	{
	$fp = fopen($filename, 'w');
	foreach ($data as $row) {
	fputcsv($fp, $row);
	}
	fclose($fp);
	}
	/**
	* Cleans a string to be used as a variable name.
	*
	* @param string $str String to clean.
	* @return string Cleaned string.
	*/
	public static function clean_str(string $str): string
	{
	return preg_replace('/[^A-Za-z0-9_]/', '', $str);
	}
	/**
	* Zips a file.
	*
	* @param string $src Path to the file to zip.
	* @param string $dest Path to the output zip file.
	* @return void
	*/
	public static function zip_file(string $src, string $dest): void
	{
	$zip = new ZipArchive();
	if ($zip->open($dest, ZipArchive::CREATE) === TRUE) {
	$zip->addFile($src, basename($src));
	$zip->close();
	}

php-dna/tests/Snps/SnpsTest.php

Lines 1 to 841 in 3d5b908

	<?php
	declare(strict_types=1);
	namespace DnaTest\Snps;
	use Dna\Snps\SNPs;
	class SnpsTest extends BaseSNPsTestCase
	{
	// private $table;
	protected function setUp(): void
	{
	parent::setUp();
	}
	public static function empty_snps()
	{
	return [new SNPs(), new SNPs(""), new SNPs("tests/input/empty.txt")];
	}
	public function test_len()
	{
	$s = new SNPs("tests/input/generic.csv");
	$this->assertEquals(count($s), 8);
	}
	public function test_len_empty()
	{
	foreach (self::empty_snps() as $s) {
	$this->assertEquals(count($s), 0);
	}
	}
	public function test__toString()
	{
	$s = new SNPs("tests/input/GRCh37.csv");
	$this->assertEquals("SNPs('GRCh37.csv')", $s->__toString());
	}
	public function test__toString_bytes()
	{
	$data = file_get_contents("tests/input/GRCh37.csv");
	$s = new SNPs($data);
	$this->assertEquals("SNPs(<bytes>)", $s->__toString());
	}
	public function testAssembly()
	{
	$s = new SNPs("tests/input/GRCh38.csv");
	$this->assertEquals($s->getAssembly(), "GRCh38");
	}
	public function testAssemblyNoSnps()
	{
	$emptySnps = $this->empty_snps();
	foreach ($emptySnps as $snps) {
	$this->assertEmpty($snps->getAssembly());
	}
	}
	public function testBuild()
	{
	$s = new SNPs("tests/input/NCBI36.csv");
	$this->assertEquals($s->getBuild(), 36);
	$this->assertEquals($s->getAssembly(), "NCBI36");
	}
	public function testBuildDetectedNoSnps()
	{
	$emptySnps = $this->empty_snps();
	foreach ($emptySnps as $snps) {
	$this->assertFalse($snps->isBuildDetected());
	}
	}
	public function testBuildNoSnps()
	{
	$emptySnps = $this->empty_snps();
	foreach ($emptySnps as $snps) {
	$this->assertEmpty($snps->getBuild());
	}
	}
	public function testBuildDetectedPARSnps()
	{
	$snps = $this->loadAssignPARSnps('tests/input/GRCh37_PAR.csv');
	$this->assertEquals(37, $snps->getBuild());
	$this->assertTrue($snps->isBuildDetected());
	$expectedSnps = $this->snps_GRCh37_PAR();
	$actualSnps = $snps->getSnps();
	$this->assertEquals($expectedSnps, $actualSnps);
	}
	public function test_notnull()
	{
	$s = new SNPs("tests/input/generic.csv");
	$snps = $this->generic_snps();
	unset($snps["rs5"]);
	$this->assertEquals($s->notnull(), $snps, "Frames are not equal!");
	}
	public function test_heterozygous()
	{
	$s = new SNPs("tests/input/generic.csv");
	$expected = $this->create_snp_df(
	rsid: ["rs6", "rs7", "rs8"],
	chrom: ["1", "1", "1"],
	pos: [106, 107, 108],
	genotype: ["GC", "TC", "AT"]
	);
	$this->assertEquals($expected, $s->heterozygous(), "Frames are not equal!");
	}
	public function test_homozygous()
	{
	$s = new SNPs("tests/input/generic.csv");
	$expected = $this->create_snp_df(
	rsid: ["rs1", "rs2", "rs3", "rs4"],
	chrom: ["1", "1", "1", "1"],
	pos: [101, 102, 103, 104],
	genotype: ["AA", "CC", "GG", "TT"],
	);
	$this->assertEquals($expected, $s->homozygous(), "Frames are not equal!");
	}
	public function test_homozygous_chrom()
	{
	$s = new SNPs("tests/input/generic.csv");
	$expected = $this->create_snp_df(
	rsid: ["rs1", "rs2", "rs3", "rs4"],
	chrom: ["1", "1", "1", "1"],
	pos: [101, 102, 103, 104],
	genotype: ["AA", "CC", "GG", "TT"],
	);
	$this->assertEquals($expected, $s->homozygous("1"), "Frames are not equal!");
	}
	public function test_valid_False()
	{
	foreach ($this->empty_snps() as $snps) {
	$this->assertFalse($snps->isValid());
	}
	}
	public function test_valid_True()
	{
	$s = new SNPs("tests/input/generic.csv");
	$this->assertTrue($s->isValid());
	}
	public function test_only_detect_source()
	{
	$s = new SNPs("tests/input/generic.csv", true);
	$this->assertEquals($s->getSource(), "generic");
	$this->assertEquals(count($s), 0);
	}
	public function test_empty_dataframe()
	{
	// for snps in self.empty_snps():
	// self.assertListEqual(
	// list(snps.snps.columns.values), ["chrom", "pos", "genotype"]
	// )
	// self.assertEqual(snps.snps.index.name, "rsid")
	// foreach ($this->empty_snps() as $snps) {
	// $this->assertEquals(
	// $snps->getSnps()->columns->toArray(),
	// ["chrom", "pos", "genotype"]
	// );
	// $this->assertEquals($snps->getSnps()->index->name, "rsid");
	// }
	}
	public function test_assembly_None()
	{
	$snps = new SNPs();
	$this->assertFalse($snps->getAssembly());
	}
	// def test_summary(self):
	// s = SNPs("tests/input/GRCh38.csv")
	// self.assertDictEqual(
	// s.summary,
	// {
	// "source": "generic",
	// "assembly": "GRCh38",
	// "build": 38,
	// "build_detected": True,
	// "count": 4,
	// "chromosomes": "1, 3",
	// "sex": "",
	// },
	// )
	public function test_summary()
	{
	$s = new SNPs("tests/input/GRCh38.csv");
	$this->assertEquals(
	$s->getSummary(),
	[
	"source" => "generic",
	"assembly" => "GRCh38",
	"build" => 38,
	"build_detected" => true,
	"count" => 4,
	"chromosomes" => "1, 3",
	"sex" => "",
	]
	);
	}
	public function test_summary_no_snps()
	{
	foreach ($this->empty_snps() as $snps) {
	$this->assertEquals($snps->getSummary(), []);
	}
	}
	public function test_chromosomes()
	{
	$s = new SNPs("tests/input/chromosomes.csv");
	var_dump($s->getChromosomes());
	$this->assertEquals(["1", "2", "3", "5", "PAR", "MT"], $s->getChromosomes());
	}
	public function test_chromosomes_no_snps()
	{
	foreach ($this->empty_snps() as $snps) {
	$this->assertEmpty($snps->getChromosomes());
	}
	}
	public function test_sex_Female_X_chrom()
	{
	$s = $this->simulate_snps(
	chrom: "X",
	pos_start: 1,
	pos_max: 155270560,
	pos_step: 10000,
	genotype: "AC"
	);
	$this->assertEquals("Female", $s->getSex());
	}
	public function test_sex_Female_Y_chrom()
	{
	$s = $this->simulate_snps(
	chrom: "Y",
	pos_start: 1,
	pos_max: 59373566,
	pos_step: 10000,
	null_snp_step: 1
	);
	$this->assertEquals("Female", $s->getSex());
	}
	// def test_sex_Male_X_chrom(self):
	// s = self.simulate_snps(
	// chrom="X", pos_start=1, pos_max=155270560, pos_step=10000, genotype="AA"
	// )
	// self.assertEqual(s.count, 15528)
	// s._deduplicate_XY_chrom()
	// self.assertEqual(s.count, 15528)
	// self.assertEqual(len(s.discrepant_XY), 0)
	// self.assertEqual(s.sex, "Male")
	public function test_sex_Male_X_chrom()
	{
	$s = $this->simulate_snps(
	chrom: "X",
	pos_start: 1,
	pos_max: 155270560,
	pos_step: 10000,
	genotype: "AA"
	);
	$this->assertEquals(15528, $s->count());
	$s->deduplicate_XY_chrom();
	$this->assertEquals(15528, $s->count());
	$this->assertEquals(0, count($s->getDiscrepantXY()));
	$this->assertEquals("Male", $s->getSex());
	}
	// def test_sex_Male_X_chrom_discrepant_XY(self):
	// s = self.simulate_snps(
	// chrom="X", pos_start=1, pos_max=155270560, pos_step=10000, genotype="AA"
	// )
	// self.assertEqual(s.count, 15528)
	// s._snps.loc["rs8001", "genotype"] = "AC"
	// s._deduplicate_XY_chrom()
	// self.assertEqual(s.count, 15527)
	// result = self.create_snp_df(
	// rsid=["rs8001"], chrom=["X"], pos=[80000001], genotype=["AC"]
	// )
	// pd.testing.assert_frame_equal(s.discrepant_XY, result, check_exact=True)
	// self.assertEqual(s.sex, "Male")
	public function test_sex_Male_X_chrom_discrepant_XY()
	{
	$s = $this->simulate_snps(
	chrom: "X",
	pos_start: 1,
	pos_max: 155270560,
	pos_step: 10000,
	genotype: "AA"
	);
	$this->assertEquals(15528, $s->count());
	// $s->getSnps()->loc["rs8001", "genotype"] = "AC";
	$s->setValue("rs8001", "genotype", "AC");
	$s->deduplicate_XY_chrom();
	$this->assertEquals(15527, $s->count());
	$result = $this->create_snp_df(
	rsid: ["rs8001"],
	chrom: ["X"],
	pos: [80000001],
	genotype: ["AC"]
	);
	$this->assertEquals($result, $s->getDiscrepantXY());
	$this->assertEquals("Male", $s->getSex());
	}
	// def test_sex_Male_Y_chrom(self):
	// s = self.simulate_snps(chrom="Y", pos_start=1, pos_max=59373566, pos_step=10000)
	// self.assertEqual(s.sex, "Male")
	public function test_sex_male_Y_chrom()
	{
	$s = $this->simulate_snps(
	chrom: "Y",
	pos_start: 1,
	pos_max: 59373566,
	pos_step: 10000
	);
	$this->assertEquals("Male", $s->getSex());
	}
	// def test_sex_not_determined(self):
	// s = self.simulate_snps(
	// chrom="1", pos_start=1, pos_max=249250621, pos_step=10000
	// )
	// self.assertEqual(s.sex, "")
	public function test_sex_not_determined()
	{
	$s = $this->simulate_snps(
	chrom: "1",
	pos_start: 1,
	pos_max: 249250621,
	pos_step: 10000
	);
	$this->assertEquals("", $s->getSex());
	}
	// def test_sex_no_snps(self):
	// for snps in self.empty_snps():
	// self.assertFalse(snps.sex)
	public function test_sex_no_snps()
	{
	foreach ($this->empty_snps() as $snps) {
	$this->assertEmpty($snps->getSex());
	}
	}
	public function test_source()
	{
	$s = new SNPs("tests/input/generic.csv");
	$this->assertEquals("generic", $s->getSource());
	$this->assertEquals(["generic"], $s->getAllSources());
	}
	public function test_source_no_snps()
	{
	foreach ($this->empty_snps() as $snps) {
	$this->assertEmpty($snps->getSource());
	}
	}
	public function test_count()
	{
	$s = new SNPs("tests/input/NCBI36.csv");
	$this->assertEquals(4, $s->count());
	}
	public function test_count_no_snps()
	{
	foreach ($this->empty_snps() as $snps) {
	$this->assertEquals(0, $snps->count());
	$this->assertEmpty($snps->getSnps());
	}
	}
	public function testDeduplicateFalse()
	{
	$snps = new SNPs("tests/input/duplicate_rsids.csv", deduplicate: false);
	$result = $this->create_snp_df(["rs1", "rs1", "rs1"], ["1", "1", "1"], [101, 102, 103], ["AA", "CC", "GG"]);
	$this->assertEquals($result, $snps->snps);
	}
	public function testDeduplicateMTChrom()
	{
	$snps = new SNPs("tests/input/ancestry_mt.txt");
	$result = $this->create_snp_df(["rs1", "rs2"], ["MT", "MT"], [101, 102], ["A", null]);
	$this->assertEquals($result, $snps->snps);
	$heterozygousMTSnps = $this->create_snp_df(["rs3"], ["MT"], [103], ["GC"]);
	$this->assertEquals($heterozygousMTSnps, $snps->heterozygous_MT);
	}
	public function testDeduplicateMTChromFalse()
	{
	$snps = new SNPs("tests/input/ancestry_mt.txt", deduplicate: false);
	$result = $this->create_snp_df(["rs1", "rs2", "rs3"], ["MT", "MT", "MT"], [101, 102, 103], ["AA", null, "GC"]);
	$this->assertEquals($result, $snps->snps);
	}
	public function testDuplicateRsids()
	{
	$snps = new SNPs("tests/input/duplicate_rsids.csv");
	$result = $this->create_snp_df(["rs1"], ["1"], [101], ["AA"]);
	$duplicate = $this->create_snp_df(["rs1", "rs1"], ["1", "1"], [102, 103], ["CC", "GG"]);
	$this->assertEquals($result, $snps->getSnps());
	$this->assertEquals($duplicate, $snps->duplicate);
	}
	public function _run_remap_test($f, $mappings)
	{
	if ($this->downloads_enabled) {
	$f();
	} else {
	$mock = $this->createMock(Resources::class);
	$mock->method('get_assembly_mapping_data')->willReturn($mappings);
	$this->getMockBuilder(Resources::class)
	->setMethods(['get_assembly_mapping_data'])
	->getMock();
	$f();
	}
	}
	public function test_remap_36_to_37()
	{
	$this->_run_remap_test(function () {
	$s = new SNPs("tests/input/NCBI36.csv");
	list($chromosomes_remapped, $chromosomes_not_remapped) = $s->remap(37);
	$this->assertEquals(37, $s->build);
	$this->assertEquals("GRCh37", $s->assembly);
	$this->assertCount(2, $chromosomes_remapped);
	$this->assertCount(0, $chromosomes_not_remapped);
	$this->assertEquals($this->snps_GRCh37(), $s->getSnps());
	}, $this->NCBI36_GRCh37());
	}
	public function test_remap_36_to_37_multiprocessing()
	{
	$this->_run_remap_test(function () {
	$s = new SNPs("tests/input/NCBI36.csv", true);
	[$chromosomes_remapped, $chromosomes_not_remapped] = $s->remap(37);
	$this->assertEquals(37, $s->build);
	$this->assertEquals("GRCh37", $s->assembly);
	$this->assertCount(2, $chromosomes_remapped);
	$this->assertCount(0, $chromosomes_not_remapped);
	$this->assertSnpsArrayEquals($s->snps, $this->snps_GRCh37(), true);
	}, $this->NCBI36_GRCh37());
	}
	public function test_remap_37_to_36()
	{
	$this->_run_remap_test(function () {
	$s = new SNPs("tests/input/GRCh37.csv");
	[$chromosomes_remapped, $chromosomes_not_remapped] = $s->remap(36);
	$this->assertEquals(36, $s->build);
	$this->assertEquals("NCBI36", $s->assembly);
	$this->assertCount(2, $chromosomes_remapped);
	$this->assertCount(0, $chromosomes_not_remapped);
	$this->assertSnpsArrayEquals($s->snps, $this->snps_NCBI36(), true);
	}, $this->GRCh37_NCBI36());
	}
	public function test_remap_37_to_38()
	{
	$this->_run_remap_test(function () {
	$s = new SNPs("tests/input/GRCh37.csv");
	[$chromosomes_remapped, $chromosomes_not_remapped] = $s->remap(38);
	$this->assertEquals(38, $s->build);
	$this->assertEquals("GRCh38", $s->assembly);
	$this->assertCount(2, $chromosomes_remapped);
	$this->assertCount(0, $chromosomes_not_remapped);
	$this->assertSnpsArrayEquals($s->snps, $this->snps_GRCh38(), true);
	}, $this->GRCh37_GRCh38());
	}
	public function test_remap_37_to_38_with_PAR_SNP()
	{
	$this->_run_remap_test(function () {
	$s = $this->loadAssignPARSNPs("tests/input/GRCh37_PAR.csv");
	$this->assertEquals(4, $s->count);
	[$chromosomes_remapped, $chromosomes_not_remapped] = $s->remap(38);
	$this->assertEquals(38, $s->build);
	$this->assertEquals("GRCh38", $s->assembly);
	$this->assertCount(2, $chromosomes_remapped);
	$this->assertCount(1, $chromosomes_not_remapped);
	$this->assertEquals(3, $s->count);
	$this->assertSnpsArrayEquals($s->snps, $this->snps_GRCh38_PAR(), true);
	}, $this->GRCh37_GRCh38_PAR());
	}
	public function test_remap_37_to_37()
	{
	$s = new SNPs("tests/input/GRCh37.csv");
	[$chromosomes_remapped, $chromosomes_not_remapped] = $s->remap(37);
	$this->assertEquals(37, $s->build);
	$this->assertEquals("GRCh37", $s->assembly);
	$this->assertCount(0, $chromosomes_remapped);
	$this->assertCount(2, $chromosomes_not_remapped);
	$this->assertSnpsArrayEquals($s->snps, $this->snps_GRCh37(), true);
	}
	public function test_remap_invalid_assembly()
	{
	$s = new SNPs("tests/input/GRCh37.csv");
	[$chromosomes_remapped, $chromosomes_not_remapped] = $s->remap(-1);
	$this->assertEquals(37, $s->build);
	$this->assertEquals("GRCh37", $s->assembly);
	$this->assertCount(0, $chromosomes_remapped);
	$this->assertCount(2, $chromosomes_not_remapped);
	}
	public function test_remap_no_snps()
	{
	$s = new SNPs();
	[$chromosomes_remapped, $chromosomes_not_remapped] = $s->remap(38);
	$this->assertFalse($s->build);
	$this->assertCount(0, $chromosomes_remapped);
	$this->assertCount(0, $chromosomes_not_remapped);
	}
	public function testSaveBufferBinary()
	{
	$s = new SNPs("tests/input/generic.csv");
	$out = fopen('php://memory', 'wb');
	$s->toTsv($out);
	rewind($out);
	$this->assertTrue(strpos(stream_get_contents($out), "# Generated by snps") === 0);
	}
	public function testSaveNoSNPs()
	{
	$s = new SNPs();
	$this->assertFalse($s->toTsv());
	}
	public function testSaveNoSNPsVCF()
	{
	$s = new SNPs();
	$this->assertFalse($s->toVcf());
	}
	public function testSaveSource()
	{
	$tmpdir = sys_get_temp_dir();
	$s = new SNPs("tests/input/GRCh38.csv", output_dir: $tmpdir);
	$dest = $tmpdir . DIRECTORY_SEPARATOR . "generic_GRCh38.txt";
	$this->assertEquals($s->toTsv(), $dest);
	$snps = new SNPs($dest);
	$this->assertEquals($snps->build, 38);
	$this->assertTrue($snps->buildDetected);
	$this->assertEquals($snps->source, "generic");
	$this->assertEquals($snps->_source, ["generic"]);
	$this->assertEquals($this->snps_GRCh38(), $snps->getSnps());
	}
	private function makeAncestryAssertions($d)
	{
	$this->assertEquals($d["population_code"], "ITU");
	$this->assertEquals($d["population_description"], "Indian Telugu in the UK");
	$this->assertIsFloat($d["population_percent"]);
	$this->assertGreaterThanOrEqual(0.2992757864426246 - 0.00001, $d["population_percent"]);
	$this->assertLessThanOrEqual(0.2992757864426246 + 0.00001, $d["population_percent"]);
	$this->assertEquals($d["superpopulation_code"], "SAS");
	$this->assertEquals($d["superpopulation_description"], "South Asian Ancestry");
	$this->assertIsFloat($d["superpopulation_percent"]);
	$this->assertGreaterThanOrEqual(0.827977563875996 - 0.00001, $d["superpopulation_percent"]);
	$this->assertLessThanOrEqual(0.827977563875996 + 0.00001, $d["superpopulation_percent"]);
	$this->assertArrayHasKey("predicted_population_population", $d["ezancestry_df"]);
	$this->assertArrayHasKey("predicted_population_superpopulation", $d["ezancestry_df"]);
	}
	// public function testAncestry()
	// {
	// $ezancestryMods = ["ezancestry", "ezancestry.commands"];
	// $poppedMods = $this->popModules($ezancestryMods);
	// if (extension_loaded("ezancestry")) {
	// // Test with ezancestry if installed
	// $s = new SNPs("tests/input/generic.csv");
	// $this->makeAncestryAssertions($s->predictAncestry());
	// }
	// // Mock ezancestry modules
	// foreach ($ezancestryMods as $mod) {
	// $this->setMockedModule($mod);
	// }
	// // Mock the predict function
	// $mockedData = [
	// "predicted_population_population" => ["ITU"],
	// "population_description" => ["Indian Telugu in the UK"],
	// "ITU" => [0.2992757864426246],
	// "predicted_population_superpopulation" => ["SAS"],
	// "superpopulation_name" => ["South Asian Ancestry"],
	// "SAS" => [0.827977563875996],
	// ];
	// $this->setMockedFunction("ezancestry.commands", "predict", $mockedData);
	// // Test with mocked ezancestry
	// $s = new SNPs("tests/input/generic.csv");
	// $this->makeAncestryAssertions($s->predictAncestry());
	// // Unload mocked ezancestry modules
	// $this->popModules($ezancestryMods);
	// // Restore ezancestry modules if ezancestry is installed
	// $this->restoreModules($poppedMods);
	// }
	public function testAncestryModuleNotFoundError()
	{
	if (!extension_loaded("ezancestry")) {
	// Test when ezancestry is not installed
	$s = new SNPs("tests/input/generic.csv");
	$this->expectException(ModuleNotFoundError::class);
	$this->expectExceptionMessage("Ancestry prediction requires the ezancestry package; please install it using `composer require ezancestry/ezancestry`");
	$s->predictAncestry();
	}
	}
	private function getChipClusters($pos = [101, 102, 103, 104, 105, 106, 107, 108], $cluster = "c1", $length = 8)
	{
	$data = [];
	for ($i = 0; $i < $length; $i++) {
	$data[] = [
	"chrom" => "1",
	"pos" => $pos[$i],
	"clusters" => $cluster
	];
	}
	return collect($data);
	}
	public function runClusterTest($f, $chipClusters)
	{
	$mock = $this->getMockBuilder(Resources::class)
	->setMethods(['getChipClusters'])
	->getMock();
	$mock->method('getChipClusters')
	->willReturn($chipClusters);
	$this->assertInstanceOf(Resources::class, $mock);
	$f($mock);
	}
	public function testCluster()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/23andme.txt", $mock);
	$this->assertEquals($s->getCluster(), "c1");
	}, $this->getChipClusters());
	}
	public function testChip()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/23andme.txt", $mock);
	$this->assertEquals($s->getChip(), "HTS iSelect HD");
	}, $this->_getChipClusters());
	}
	public function testChipVersion()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/23andme.txt", $mock);
	$this->assertEquals($s->getChipVersion(), "v4");
	}, $this->getChipClusters());
	}
	public function testChipVersionNA()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/myheritage.csv", $mock);
	$this->assertEquals($s->getCluster(), "c3");
	$this->assertEquals($s->getChipVersion(), "");
	}, $this->getChipClusters("c3"));
	}
	public function testComputeClusterOverlapSetPropertyValues()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/23andme.txt", $mock);
	$s->computeClusterOverlap();
	$this->assertEquals($s->getCluster(), "c1");
	$this->assertEquals($s->getChip(), "HTS iSelect HD");
	$this->assertEquals($s->getChipVersion(), "v4");
	}, $this->_getChipClusters());
	}
	public function testComputeClusterOverlapThresholdNotMet()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/23andme.txt", $mock);
	$this->assertEquals($s->getCluster(), "");
	}, $this->_getChipClusters(range(104, 112)));
	}
	public function testComputeClusterOverlapSourceWarning()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/generic.csv", $mock);
	$this->assertEquals($s->getCluster(), "c1");
	}, $this->_getChipClusters());
	$logs = $this->getActualOutput();
	$this->assertStringContainsString(
	"Detected SNPs data source not found in cluster's company composition",
	$logs
	);
	}
	public function testComputeClusterOverlapRemap()
	{
	$this->runClusterTest(function ($mock) {
	$s = new SNPs("tests/input/23andme.txt", $mock);
	// drop SNPs not currently remapped by test mapping data
	$snps = $s->getSnps();
	unset($snps["rs4"]);
	unset($snps["rs5"]);
	unset($snps["rs6"]);
	unset($snps["rs7"]);
	unset($snps["rs8"]);
	$s->setBuild(36); // manually set build 36
	$this->assertEquals($s->getCluster(), "c1");
	$this->assertEquals($s->getBuild(), 36); // ensure copy gets remapped
	}, $this->_getChipClusters(["pos" => range(101, 104)], 3));
	}
	public function testSnpsQc()
	{
	// Simulate the creation of your SNP object with the provided CSV data
	$s = new SNPs("tests/input/generic.csv");
	// Identify quality controlled SNPs and get them as an array or other data structure
	$snpsQc = $s->getSnpsQc();
	// Create an array that represents your expected QC SNPs, excluding rs4 and rs6
	$expectedQcSnps = $this->genericSnps();
	unset($expectedQcSnps['rs4']);
	unset($expectedQcSnps['rs6']);
	// Assert that the computed QC SNPs match the expected QC SNPs
	$this->assertEquals($expectedQcSnps, $snpsQc);
	}
	public function testLowQuality()
	{
	// Simulate the creation of your SNP object with the provided CSV data
	$s = new SNPs("tests/input/generic.csv");
	// Identify low-quality SNPs and get them as an array or other data structure
	$lowQualitySnps = $s->getLowQualitySnps();
	// Create an array that represents your expected low-quality SNPs, including rs4 and rs6
	$expectedLowQualitySnps = $this->genericSnps();
	// Assert that the computed low-quality SNPs match the expected low-quality SNPs
	$this->assertEquals($expectedLowQualitySnps, $lowQualitySnps);
	}
	// public function testSnpsQcLowQualityNoCluster() {
	// function f() {
	// $s = new SNPs("tests/input/generic.csv");
	// // Identify low-quality SNPs
	// $this->assertEquals(
	// $s->low_quality,
	// $this->getLowQualitySnps(['rs4', 'rs6'])
	// );
	// // Return already identified low-quality SNPs (test branch)
	// $this->assertEquals(
	// $s->low_quality,
	// $this->getLowQualitySnps(['rs4', 'rs6'])
	// );
	// }
	// $this->runLowQualitySnpsTest('f', $this->getLowQualitySnps(), ['cluster' => '']);
	// }
	// private function testIdentifyLowQualitySnpsRemap() {
	// $f = function() {
	// $s = new SNPs("tests/input/generic.csv");
	// // Drop SNPs not currently remapped by test mapping data
	// $s->_snps->drop(["rs4", "rs5", "rs6", "rs7", "rs8"], 1);
	// $s->_build = 36; // Manually set build 36
	// $s->identifyLowQualitySnps();
	// $this->assertEquals($s->snpsQc, $this->getLowQualitySnps(['rs1', 'rs3']));
	// $this->assertEquals($s->lowQuality, $this->getLowQualitySnps()['rs2']);
	// $this->assertEquals($s->build, 36); // Ensure copy gets remapped
	// }
	// $mock = $this->getMockBuilder('Resources')
	// ->setMethods(['getAssemblyMappingData'])
	// ->getMock();
	// $mock->expects($this->any())
	// ->method('getAssemblyMappingData')
	// ->willReturn($this->getTestAssemblyMappingData(
	// "NCBI36",
	// "GRCh37",
	// array_fill(0, 8, 1),
	// array(101, 101, 102, 102, 103, 103, 0, 0)
	// ));
	// $this->runLowQualitySnpsTest('f', $this->getLowQualitySnps(array(102, 1001)));
	// }

---

Step 2: ⌨️ Coding

• Modify src/Individual.php ✓ f3f7a9c Edit

Modify src/Individual.php with contents: Rename private properties and methods to follow PSR naming conventions.

<original_code>
private string $_name;

public function __construct(string $name, mixed $raw_data = [], array $kwargs = [])
{
    /**
     * Initialize an ``Individual`` object.
     *
     * Parameters
     * ----------
     * name : str
     *     name of the individual
     * raw_data : str, bytes, ``SNPs`` (or list or tuple thereof)
     *     path(s) to file(s), bytes, or ``SNPs`` object(s) with raw genotype data
     * kwargs : array
     *     parameters to ``snps.SNPs`` and/or ``snps.SNPs.merge``
     */
    $this->_name = $name;

    $init_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs);
    $merge_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, ''), $kwargs);

</original_code>

<new_code>
private string $name;

public function __construct(string $name, mixed $rawData = [], array $kwargs = [])
{
    /**
     * Initialize an ``Individual`` object.
     *
     * @param string $name Name of the individual
     * @param mixed $rawData Path(s) to file(s), bytes, or ``SNPs`` object(s) with raw genotype data
     * @param array $kwargs Parameters to ``snps.SNPs`` and/or ``snps.SNPs.merge``
     */
    $this->name = $name;

    $initArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs);
    $mergeArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, 'merge'), $kwargs);

</new_code>

• Modify src/Individual.php ✓ f3f7a9c Edit

Modify src/Individual.php with contents: Add type hints, return type declarations, and docblock comments to all methods.

<original_code>
private function _get_defined_kwargs(ReflectionMethod $callable, array $kwargs): array
{
$parameters = $callable->getParameters();
$defined_kwargs = [];
foreach ($parameters as $parameter) {
$name = $parameter->getName();
if (array_key_exists($name, $kwargs)) {
$defined_kwargs[$name] = $kwargs[$name];
}
}

    return $defined_kwargs;
}

public function __toString(): string
{
    return sprintf("Individual('%s')", $this->_name);
}

public function getName(): string
{
    /**
     * Get this ``Individual``'s name.
     *
     * Returns
     * -------
     * str
     */
    return $this->_name;
}

public function getVarName(): string
{
    return clean_str($this->_name);
}

</original_code>

<new_code>
/**
* Get defined keyword arguments for a method
*
* @param ReflectionMethod $method The method to get arguments for
* @param array $kwargs The keyword arguments to filter
* @return array The defined keyword arguments
*/
private function getDefinedKwargs(ReflectionMethod $method, array $kwargs): array
{
$parameters = $method->getParameters();
$definedKwargs = [];
foreach ($parameters as $parameter) {
$name = $parameter->getName();
if (array_key_exists($name, $kwargs)) {
$definedKwargs[$name] = $kwargs[$name];
}
}

    return $definedKwargs;
}

/**
 * Get the string representation of the Individual
 *
 * @return string The string representation
 */
public function __toString(): string
{
    return sprintf("Individual('%s')", $this->name);
}

/**
 * Get the Individual's name
 *
 * @return string The name
 */
public function getName(): string
{
    return $this->name;
}

/**
 * Get a variable-safe version of the Individual's name
 *
 * @return string The variable-safe name
 */
public function getVarName(): string
{
    return clean_str($this->name);
}

</new_code>

• Modify src/Individual.php ✓ f3f7a9c Edit

Modify src/Individual.php with contents: Simplify constructor logic and use more descriptive variable names.

<original_code>
public function __construct(string $name, mixed $raw_data = [], array $kwargs = [])
{
/**
* Initialize an Individual object.
*
* Parameters
* ----------
* name : str
* name of the individual
* raw_data : str, bytes, SNPs (or list or tuple thereof)
* path(s) to file(s), bytes, or SNPs object(s) with raw genotype data
* kwargs : array
* parameters to snps.SNPs and/or snps.SNPs.merge
*/
$this->_name = $name;

    $init_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs);
    $merge_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, ''), $kwargs);

    parent::__construct(...array_values($init_args));

    if (!is_array($raw_data)) {
        $raw_data = [$raw_data];
    }

    foreach ($raw_data as $file) {
        $s = $file instanceof SNPs ? $file : new SNPs($file, ...array_values($init_args));
        $this->merge([$s], ...array_values($merge_args));
    }
}

</original_code>

<new_code>
/**
* Initialize an Individual object
*
* @param string $name Name of the individual
* @param mixed $rawData Path(s) to file(s), bytes, or SNPs object(s) with raw genotype data
* @param array $kwargs Parameters to snps.SNPs and/or snps.SNPs.merge
*/
public function __construct(string $name, mixed $rawData = [], array $kwargs = [])
{
$this->name = $name;

    $snpsConstructorArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs);
    $snpsMergeArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, 'merge'), $kwargs);

    parent::__construct(...array_values($snpsConstructorArgs));

    $rawDataArray = is_array($rawData) ? $rawData : [$rawData];

    foreach ($rawDataArray as $data) {
        $snps = $data instanceof SNPs ? $data : new SNPs($data, ...array_values($snpsConstructorArgs));
        $this->merge([$snps], ...array_values($snpsMergeArgs));
    }
}

</new_code>

• Modify src/Individual.php ✓ f3f7a9c Edit

Modify src/Individual.php with contents: Extract logic for creating SNPs objects into a separate private method.

<original_code>
public function __construct(string $name, mixed $raw_data = [], array $kwargs = [])
{
/**
* Initialize an Individual object.
*
* Parameters
* ----------
* name : str
* name of the individual
* raw_data : str, bytes, SNPs (or list or tuple thereof)
* path(s) to file(s), bytes, or SNPs object(s) with raw genotype data
* kwargs : array
* parameters to snps.SNPs and/or snps.SNPs.merge
*/
$this->_name = $name;

    $init_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs);
    $merge_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, ''), $kwargs);

    parent::__construct(...array_values($init_args));

    if (!is_array($raw_data)) {
        $raw_data = [$raw_data];
    }

    foreach ($raw_data as $file) {
        $s = $file instanceof SNPs ? $file : new SNPs($file, ...array_values($init_args));
        $this->merge([$s], ...array_values($merge_args));
    }
}

</original_code>

<new_code>
/**
* Initialize an Individual object
*
* @param string $name Name of the individual
* @param mixed $rawData Path(s) to file(s), bytes, or SNPs object(s) with raw genotype data
* @param array $kwargs Parameters to snps.SNPs and/or snps.SNPs.merge
*/
public function __construct(string $name, mixed $rawData = [], array $kwargs = [])
{
$this->name = $name;

    $snpsConstructorArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs);
    $snpsMergeArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, 'merge'), $kwargs);

    parent::__construct(...array_values($snpsConstructorArgs));

    $rawDataArray = is_array($rawData) ? $rawData : [$rawData];

    foreach ($rawDataArray as $data) {
        $snps = $this->createSnpsObject($data, $snpsConstructorArgs);
        $this->merge([$snps], ...array_values($snpsMergeArgs));
    }
}

/**
 * Create an SNPs object from raw data
 *
 * @param mixed $data The raw data (file path, bytes, or SNPs object)
 * @param array $constructorArgs The constructor arguments for the SNPs object
 * @return SNPs The created SNPs object
 */
private function createSnpsObject(mixed $data, array $constructorArgs): SNPs
{
    return $data instanceof SNPs ? $data : new SNPs($data, ...array_values($constructorArgs));
}

</new_code>

• Modify src/Individual.php ✓ f3f7a9c Edit

Modify src/Individual.php with contents: Fix indentation, add blank lines, ensure opening braces are on same line, add spaces around operators.

<original_code>

_name = $name; $init_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs); $merge_args = $this->_get_defined_kwargs(new ReflectionMethod(SNPs::class, ''), $kwargs); parent::__construct(...array_values($init_args)); if (!is_array($raw_data)) { $raw_data = [$raw_data]; } foreach ($raw_data as $file) { $s = $file instanceof SNPs ? $file : new SNPs($file, ...array_values($init_args)); $this->merge([$s], ...array_values($merge_args)); } } private function _get_defined_kwargs(ReflectionMethod $callable, array $kwargs): array { $parameters = $callable->getParameters(); $defined_kwargs = []; foreach ($parameters as $parameter) { $name = $parameter->getName(); if (array_key_exists($name, $kwargs)) { $defined_kwargs[$name] = $kwargs[$name]; } } return $defined_kwargs; } public function __toString(): string { return sprintf("Individual('%s')", $this->_name); } public function getName(): string { /** * Get this ``Individual``'s name. * * Returns * ------- * str */ return $this->_name; } public function getVarName(): string { return clean_str($this->_name); } } name = $name; $snpsConstructorArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, '__construct'), $kwargs); $snpsMergeArgs = $this->getDefinedKwargs(new ReflectionMethod(SNPs::class, 'merge'), $kwargs); parent::__construct(...array_values($snpsConstructorArgs)); $rawDataArray = is_array($rawData) ? $rawData : [$rawData]; foreach ($rawDataArray as $data) { $snps = $this->createSnpsObject($data, $snpsConstructorArgs); $this->merge([$snps], ...array_values($snpsMergeArgs)); } } /** * Get defined keyword arguments for a method * * @param ReflectionMethod $method The method to get arguments for * @param array $kwargs The keyword arguments to filter * @return array The defined keyword arguments */ private function getDefinedKwargs(ReflectionMethod $method, array $kwargs): array { $parameters = $method->getParameters(); $definedKwargs = []; foreach ($parameters as $parameter) { $name = $parameter->getName(); if (array_key_exists($name, $kwargs)) { $definedKwargs[$name] = $kwargs[$name]; } } return $definedKwargs; } /** * Create an SNPs object from raw data * * @param mixed $data The raw data (file path, bytes, or SNPs object) * @param array $constructorArgs The constructor arguments for the SNPs object * @return SNPs The created SNPs object */ private function createSnpsObject(mixed $data, array $constructorArgs): SNPs { return $data instanceof SNPs ? $data : new SNPs($data, ...array_values($constructorArgs)); } /** * Get the string representation of the Individual * * @return string The string representation */ public function __toString(): string { return sprintf("Individual('%s')", $this->name); } /** * Get the Individual's name * * @return string The name */ public function getName(): string { return $this->name; } /** * Get a variable-safe version of the Individual's name * * @return string The variable-safe name */ public function getVarName(): string { return clean_str($this->name); } }

--- ## Step 3: 🔁 Code Review I have finished reviewing the code for completeness. I did not find errors for [`sweep/refactor_generally_to_improve_quality_th_42ca9`](https://github.com/liberu-genealogy/php-dna/commits/sweep/refactor_generally_to_improve_quality_th_42ca9). ---

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💡 To recreate the pull request edit the issue title or description. ^{Something wrong? [Let us know](https://community.sweep.dev/).} *This is an automated message generated by [Sweep AI](https://sweep.dev).*